Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase
Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase
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类异戊二烯构件的组装机制 1. 阐明香叶基焦磷酸合酶中底物结合的结构基序
DOI：
10.1021/ct500607n
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发表时间：
2014-11-01
影响因子：
5.5
通讯作者：
Xu, Jun
中科院分区：
文献类型：
--
作者：
Liu, Zhihong;Zhou, Jingwei;Xu, Jun
萜烯(类异戊二烯)是最具功能和结构多样性的天然产物。异戊烯基二磷酸(IPP)和二甲基烯丙基二磷酸(DMAPP或DPP)是由异戊烯基二磷酸(IPP)和二甲基烯丙基二磷酸(DPP)两个组成单元通过戊基转移酶(PTS)组装而成的。香叶基焦磷酸合成酶(GPPS)是在类异戊二烯生物合成过程中，在链延长的第一步合成DPP和IPP的酶。GPPS组装萜类前体的机制尚不清楚；阐明这一机制将有助于开发新的技术来生成新型天然产物类支架。通过经典和QM/MM分子动力学模拟，观察到催化口袋在其大亚基(LSU)处的开闭构象变化，并确定了Asp91(环1)和Lys239(环2)之间的关键盐桥。盐桥负责打开或关闭催化袋。同时，小亚基(SSU)调节疏水口袋的大小和形状，以灵活地承载不同形状和大小的底物(DPP/GPP/FPP，C-5/C-10/C-15)。进一步的QM/MM分子动力学模拟研究了GPPS对不同底物的结合模式。我们的模拟表明，关键残基(Asp91、Lys239和Gln156)是很好的定点突变候选者，可能有助于蛋白质工程。
Terpenes (isoprenoids) represent the most functionally and structurally diverse group of natural products. Terpenes are assembled from two building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP or DPP), by prenyltransferases (PTSs). Geranyl pyrophosphate synthase (GPPS) is the enzyme that assembles DPP and IPP in the first step of chain elongation during isoprenoid biosynthesis. The mechanism by which GPPS assembles the terpene precursor remains unknown; elucidating this mechanism will help in development of new technology to generate novel natural product-like scaffolds. With classic and QM/MM MD simulations, an open-closed conformation change of the catalytic pocket was observed in the GPPS active site at its large subunit (LSU), and a critical salt bridge between Asp91(in loop 1) and Lys239(in loop 2) was identified. The salt bridge is responsible for opening or closing the catalytic pocket. Meanwhile, the small subunit (SSU) regulates the size and shape of the hydrophobic pocket to flexibly host substrates with different shapes and sizes (DPP/GPP/FPP, C-5/C-10/C-15). Further QM/MM MD simulations were carried out to explore the binding modes for the different substrates catalyzed by GPPS. Our simulations suggest that the key residues (Asp91, Lys239, and Gln156) are good candidates for site-directed mutagenesis and may help in protein engineering.